Providing intrinsic clustering quality indices #196
Annotations
3 errors
|
../../../.julia/packages/Documenter/nQAq5/src/utilities/utilities.jl#L44
failed to run `@example` block in source/validate.md:156-182
```@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 = [:silhouettes, :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 =
MethodError: no method matching eachcol(::typeof(StatsAPI.weights))
Closest candidates are:
eachcol(!Matched::AbstractMatrix)
@ Base slicearray.jl:203
eachcol(!Matched::AbstractVector)
@ Base slicearray.jl:204
eachcol(!Matched::DataFrames.AbstractDataFrame)
@ DataFrames ~/.julia/packages/DataFrames/58MUJ/src/abstractdataframe/iteration.jl:238
Stacktrace:
[1] _cluquality_calinski_harabasz(metric::Distances.SqEuclidean, data::Matrix{Float64}, centers::Matrix{Float64}, assignments::Vector{Int64}, fuzziness::Nothing)
@ Clustering ~/work/Clustering.jl/Clustering.jl/src/clustering_quality.jl:234
[2] clustering_quality(data::Matrix{Float64}, centers::Matrix{Float64}, assignments::Vector{Int64}; quality_index::Symbol, metric::Distances.SqEuclidean)
@ Clustering ~/work/Clustering.jl/Clustering.jl/src/clustering_quality.jl:76
[3] clustering_quality
@ ~/work/Clustering.jl/Clustering.jl/src/clustering_quality.jl:54 [inlined]
[4] #clustering_quality#40
@ ~/work/Clustering.jl/Clustering.jl/src/clustering_quality.jl:90 [inlined]
[5] clustering_quality
@ ~/work/Clustering.jl/Clustering.jl/src/clustering_quality.jl:90 [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{KmeansResult{Matrix{Float64}, Float64, Int64}}}})
@ Base.Broadcast ./broadcast.jl:873
[12] (::Main.__atexample__300.var"#1#2")(qidx::Symbol)
@ Main.__atexample__300 ./none:0
[13] iterate
@ ./generator.jl:47 [inlined]
[14] _all(f::Base.var"#372#374", itr::Base.Generator{Vector{Symbol}, Main.__atexample__300.var"#1#2"}, #unused#::Colon)
@ Base ./reduce.jl:1292
[15] all
@ ./reduce.jl:1278 [inlined]
[16] Dict(kv::Base.Generator{Vector{Symbol}, Main.__atexample__300.var"#1#2"})
@ Base ./dict.jl:111
[17] top-level scope
@ validate.md:165
[18] eval
@ ./boot.jl:370 [inlined]
[19] #54
@ ~/.julia/packages/Documenter/nQAq5/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/nQAq5/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.j
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|
../../../.julia/packages/Documenter/nQAq5/src/utilities/utilities.jl#L44
failed to run `@example` block in source/validate.md:185-213
```@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
fuzzy_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 = fuzziness, quality_index = qidx)
for qidx in fuzzy_indices
)
p = [
plot(2:5, fuzzy_cmeans_quality[qidx],
marker = :circle,
title = string.(qidx),
label = nothing,
)
for qidx in fuzzy_indices
]
plot(p...,
layout = (2,1),
plot_title = "Quality indices for various number of clusters"
)
```
exception =
MethodError: no method matching eachcol(::typeof(StatsAPI.weights))
Closest candidates are:
eachcol(!Matched::AbstractMatrix)
@ Base slicearray.jl:203
eachcol(!Matched::AbstractVector)
@ Base slicearray.jl:204
eachcol(!Matched::DataFrames.AbstractDataFrame)
@ DataFrames ~/.julia/packages/DataFrames/58MUJ/src/abstractdataframe/iteration.jl:238
Stacktrace:
[1] _cluquality_calinski_harabasz(metric::Distances.SqEuclidean, data::Matrix{Float64}, centers::Matrix{Float64}, assignments::Matrix{Float64}, fuzziness::Int64)
@ Clustering ~/work/Clustering.jl/Clustering.jl/src/clustering_quality.jl:234
[2] clustering_quality(data::Matrix{Float64}, centers::Matrix{Float64}, weights::Matrix{Float64}; quality_index::Symbol, fuzziness::Int64, metric::Distances.SqEuclidean)
@ Clustering ~/work/Clustering.jl/Clustering.jl/src/clustering_quality.jl:118
[3] clustering_quality(data::Matrix{Float64}, R::FuzzyCMeansResult{Float64}; quality_index::Symbol, fuzziness::Int64, metric::Distances.SqEuclidean)
@ Clustering ~/work/Clustering.jl/Clustering.jl/src/clustering_quality.jl:126
[4] (::Base.Broadcast.var"#43#44"{Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:fuzziness, :quality_index), Tuple{Int64, Symbol}}}, typeof(clustering_quality)})(::Matrix{Float64}, ::Vararg{Any})
@ Base.Broadcast ./broadcast.jl:1297
[5] _broadcast_getindex_evalf
@ ./broadcast.jl:683 [inlined]
[6] _broadcast_getindex
@ ./broadcast.jl:656 [inlined]
[7] getindex
@ ./broadcast.jl:610 [inlined]
[8] copy
@ ./broadcast.jl:912 [inlined]
[9] materialize(bc::Base.Broadcast.Broadcasted{Base.Broadcast.DefaultArrayStyle{1}, Nothing, Base.Broadcast.var"#43#44"{Base.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:fuzziness, :quality_index), Tuple{Int64, Symbol}}}, typeof(clustering_quality)}, Tuple{Base.RefValue{Matrix{Float64}}, Vector{FuzzyCMeansResult{Float64}}}})
@ Base.Broadcast ./broadcast.jl:873
[10] (::Main.__atexample__301.var"#1#2")(qidx::Symbol)
@ Main.__atexample__301 ./none:0
[11] iterate
@ ./generator.jl:47 [inlined]
[12] _all(f::Base.var"#372#374", itr::Base.Generator{Vector{Symbol}, Main.__atexample__301.var"#1#2"}, #unused#::Colon)
@ Base ./reduce.jl:1282
[13] all
@ ./reduce.jl:1278 [inlined]
[14] Dict(kv::Base.Generator{Vector{Symbol}, Main.__atexample__301.var"#1#2"})
@ Base ./dict.jl:111
[15] top-level scope
@ validate.md:195
[16] eval
@ ./boot.jl:370 [inlined]
[17] #54
@ ~/.julia/packages/Documenter/nQAq5/src/expander_pipeline.jl:738 [inlined]
[18] cd(f::Documenter.var"#54#56"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[19] (::Documenter.var"#53#55"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/nQAq5/src/expander_pipeline.jl:737
[20] (::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/IOCapt
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