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Providing intrinsic clustering quality indices #173

Providing intrinsic clustering quality indices

Providing intrinsic clustering quality indices #173

Triggered via pull request October 9, 2023 22:34
@jakslejaksle
synchronize #257
master
Status Failure
Total duration 12m 26s
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4 errors
Julia 1.0 - ubuntu-latest - x64
Process completed with exit code 1.
Documentation: ../../../.julia/packages/Documenter/9kOxY/src/utilities/utilities.jl#L44
failed to run `@example` block in source/validate.md:134-160 ```@example using Plots, Clustering X = hcat([4., 5.] .+ 0.4 * randn(2, 10), [9., -5.] .+ 0.4 * randn(2, 5), [-4., -9.] .+ 1 * randn(2, 5)) clusterings = kmeans.(Ref(X), 2:5) hard_indices = [:silhouette, :calinski_harabasz, :xie_beni, :davies_bouldin, :dunn] kmeans_quality = Dict(qidx => clustering_quality.(Ref(X), clusterings, quality_index = qidx) for qidx in hard_indices ) p = [ plot(2:5, kmeans_quality[qidx], marker = :circle, title = string.(qidx), label = nothing, ) for qidx in hard_indices ] plot(p..., layout = (3,2), plot_title = "Quality indices for various number of clusters" ) ``` exception = ArgumentError: Quality index silhouette not supported. Stacktrace: [1] clustering_quality(X::Matrix{Float64}, centers::Matrix{Float64}, assignments::Vector{Int64}, distance::Distances.SqEuclidean; quality_index::Symbol) @ Clustering ~/work/Clustering.jl/Clustering.jl/src/clustering_quality.jl:59 [2] clustering_quality @ ~/work/Clustering.jl/Clustering.jl/src/clustering_quality.jl:29 [inlined] [3] #clustering_quality#40 @ ~/work/Clustering.jl/Clustering.jl/src/clustering_quality.jl:64 [inlined] [4] clustering_quality (repeats 2 times) @ ~/work/Clustering.jl/Clustering.jl/src/clustering_quality.jl:64 [inlined] [5] #43 @ ./broadcast.jl:1297 [inlined] [6] _broadcast_getindex_evalf @ ./broadcast.jl:683 [inlined] [7] _broadcast_getindex @ ./broadcast.jl:656 [inlined] [8] getindex @ ./broadcast.jl:610 [inlined] [9] copy(bc::Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{1}, Tuple{Base.OneTo{Int64}}, Base.Broadcast.var"#43#44"{Base.Pairs{Symbol, Symbol, Tuple{Symbol}, NamedTuple{(:quality_index,), Tuple{Symbol}}}, typeof(clustering_quality)}, Tuple{Base.RefValue{Matrix{Float64}}, Vector{KmeansResult{Matrix{Float64}, Float64, Int64}}}}) @ Base.Broadcast ./broadcast.jl:912 [10] materialize(bc::Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{1}, Nothing, Base.Broadcast.var"#43#44"{Base.Pairs{Symbol, Symbol, Tuple{Symbol}, NamedTuple{(:quality_index,), Tuple{Symbol}}}, typeof(clustering_quality)}, Tuple{Base.RefValue{Matrix{Float64}}, Vector{KmeansResult{Matrix{Float64}, Float64, Int64}}}}) @ Base.Broadcast ./broadcast.jl:873 [11] (::Main.__atexample__300.var"#1#2")(qidx::Symbol) @ Main.__atexample__300 ./none:0 [12] iterate @ ./generator.jl:47 [inlined] [13] _all(f::Base.var"#372#374", itr::Base.Generator{Vector{Symbol}, Main.__atexample__300.var"#1#2"}, #unused#::Colon) @ Base ./reduce.jl:1282 [14] all @ ./reduce.jl:1278 [inlined] [15] Dict(kv::Base.Generator{Vector{Symbol}, Main.__atexample__300.var"#1#2"}) @ Base ./dict.jl:111 [16] top-level scope @ validate.md:143 [17] eval @ ./boot.jl:370 [inlined] [18] #54 @ ~/.julia/packages/Documenter/9kOxY/src/expander_pipeline.jl:738 [inlined] [19] cd(f::Documenter.var"#54#56"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [20] (::Documenter.var"#53#55"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/9kOxY/src/expander_pipeline.jl:737 [21] (::IOCapture.var"#3#5"{DataType, Documenter.var"#53#55"{Documenter.Page, Module, Expr}, Task, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/8Uj7o/src/IOCapture.jl:119 [22] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:514 [23] with_logger @ ./logging.jl:626 [inlined] [24] capture(f::Documenter.var"#53#55"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool) @ IOCapture ~/.julia/packages/IOCapture/8Uj7o/src/IOCapture.jl:116 [25] runner(#unused#::Type{Documenter.Expa
Documentation: ../../../.julia/packages/Documenter/9kOxY/src/utilities/utilities.jl#L44
failed to run `@example` block in source/validate.md:163-191 ```@example using Plots, Clustering X = hcat([4., 5.] .+ 0.4 * randn(2, 10), [9., -5.] .+ 0.4 * randn(2, 5), [-4., -9.] .+ 1 * randn(2, 5)) fuzziness = 2 soft_indices = [:calinski_harabasz, :xie_beni] fuzzy_clusterings = fuzzy_cmeans.(Ref(X), 2:5, fuzziness) fuzzy_cmeans_quality = Dict(qidx => clustering_quality.(Ref(X), fuzzy_clusterings, fuzziness, quality_index = qidx) for qidx in soft_indices ) p = [ plot(2:5, fuzzy_cmeans_quality[qidx], marker = :circle, title = string.(qidx), label = nothing, ) for qidx in soft_indices ] plot(p..., layout = (2,1), plot_title = "Quality indices for various number of clusters" ) ``` exception = UndefVarError: `inner_inertia` not defined Stacktrace: [1] _cluquality_calinski_harabasz(X::Matrix{Float64}, centers::Matrix{Float64}, weights::Matrix{Float64}, fuzziness::Int64, distance::Distances.SqEuclidean) @ Clustering ~/work/Clustering.jl/Clustering.jl/src/clustering_quality.jl:243 [2] clustering_quality(X::Matrix{Float64}, centers::Matrix{Float64}, weights::Matrix{Float64}, fuzziness::Int64, distance::Distances.SqEuclidean; quality_index::Symbol) @ Clustering ~/work/Clustering.jl/Clustering.jl/src/clustering_quality.jl:111 [3] clustering_quality @ ~/work/Clustering.jl/Clustering.jl/src/clustering_quality.jl:89 [inlined] [4] #clustering_quality#42 @ ~/work/Clustering.jl/Clustering.jl/src/clustering_quality.jl:119 [inlined] [5] clustering_quality (repeats 2 times) @ ~/work/Clustering.jl/Clustering.jl/src/clustering_quality.jl:119 [inlined] [6] #43 @ ./broadcast.jl:1297 [inlined] [7] _broadcast_getindex_evalf @ ./broadcast.jl:683 [inlined] [8] _broadcast_getindex @ ./broadcast.jl:656 [inlined] [9] getindex @ ./broadcast.jl:610 [inlined] [10] copy @ ./broadcast.jl:912 [inlined] [11] materialize(bc::Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{1}, Nothing, Base.Broadcast.var"#43#44"{Base.Pairs{Symbol, Symbol, Tuple{Symbol}, NamedTuple{(:quality_index,), Tuple{Symbol}}}, typeof(clustering_quality)}, Tuple{Base.RefValue{Matrix{Float64}}, Vector{FuzzyCMeansResult{Float64}}, Int64}}) @ Base.Broadcast ./broadcast.jl:873 [12] (::Main.__atexample__301.var"#1#2")(qidx::Symbol) @ Main.__atexample__301 ./none:0 [13] iterate @ ./generator.jl:47 [inlined] [14] _all(f::Base.var"#372#374", itr::Base.Generator{Vector{Symbol}, Main.__atexample__301.var"#1#2"}, #unused#::Colon) @ Base ./reduce.jl:1282 [15] all @ ./reduce.jl:1278 [inlined] [16] Dict(kv::Base.Generator{Vector{Symbol}, Main.__atexample__301.var"#1#2"}) @ Base ./dict.jl:111 [17] top-level scope @ validate.md:173 [18] eval @ ./boot.jl:370 [inlined] [19] #54 @ ~/.julia/packages/Documenter/9kOxY/src/expander_pipeline.jl:738 [inlined] [20] cd(f::Documenter.var"#54#56"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [21] (::Documenter.var"#53#55"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/9kOxY/src/expander_pipeline.jl:737 [22] (::IOCapture.var"#3#5"{DataType, Documenter.var"#53#55"{Documenter.Page, Module, Expr}, Task, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/8Uj7o/src/IOCapture.jl:119 [23] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:514 [24] with_logger @ ./logging.jl:626 [inlined] [25] capture(f::Documenter.var"#53#55"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool) @ IOCapture ~/.julia/packages/IOCapture/8Uj7o/src/IOCapture.jl:116 [26] runner(#unused#::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Doc
Documentation
Process completed with exit code 1.