Process completed with exit code 1.

failed to run `@example` block in src/generated/tutorial/lmm_clusterdepth.md:80-90 ```@example lmm_clusterdepth coefficient = 2 pvalues( MersenneTwister(1), m, data_e, coefficient; n_permutations = 10, clusterforming_threshold = 1.8, ) ``` exception = MethodError: no method matching pvalues(::Random.MersenneTwister, ::UnfoldMixedModelsExt.UnfoldLinearMixedModel{Float64}, ::Array{Float64, 3}, ::Int64; n_permutations::Int64, clusterforming_threshold::Float64) The function `pvalues` exists, but no method is defined for this combination of argument types. Closest candidates are: pvalues(!Matched::Vector{MixedModels.LikelihoodRatioTest}) got unsupported keyword arguments "n_permutations", "clusterforming_threshold" @ UnfoldMixedModelsExt ~/.julia/packages/Unfold/cAmug/ext/UnfoldMixedModelsExt/statistics.jl:79 Stacktrace: [1] pvalues(::Random.MersenneTwister, ::Vararg{Any}; kwargs::@kwargs{n_permutations::Int64, clusterforming_threshold::Float64}) @ Unfold ~/.julia/packages/Unfold/cAmug/src/Unfold.jl:122 [2] top-level scope @ lmm_clusterdepth.md:82 [3] eval @ ./boot.jl:430 [inlined] [4] #60 @ ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:803 [inlined] [5] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [6] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:802 [7] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [8] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:522 [9] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger) @ Base.CoreLogging ./logging/logging.jl:632 [10] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [11] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:801

failed to run `@example` block in src/generated/tutorial/two_stage_analysis.md:133-150 ```@example two_stage_analysis # Specify the predictors of interest predictor_dict = Dict(:continuous => range(0, 2, length = 3)) # Compute the marginal effects for all subjects separately effects_all_subjects = combine( groupby(models, :subject), :unfoldmodel => (m -> effects(predictor_dict, m[1])) => AsTable, ) # Aggregate the marginal effects (per event type, time point and channel) over subjects # using the mean as aggregation function aggregated_effects = @chain effects_all_subjects begin groupby([:basisname, :channel, collect(keys(predictor_dict))..., :time]) combine(:yhat .=> [x -> mean(skipmissing(x))] .=> Symbol("yhat_", mean)) end; first(aggregated_effects, 5) ``` exception = ArgumentError: column name :basisname not found in the data frame Stacktrace: [1] lookupname @ ~/.julia/packages/DataFrames/kcA9R/src/other/index.jl:431 [inlined] [2] getindex @ ~/.julia/packages/DataFrames/kcA9R/src/other/index.jl:440 [inlined] [3] (::DataFrames.var"#35#36"{DataFrames.Index})(i::Symbol) @ DataFrames ./none:0 [4] iterate @ ./generator.jl:48 [inlined] [5] collect(itr::Base.Generator{Vector{Symbol}, DataFrames.var"#35#36"{DataFrames.Index}}) @ Base ./array.jl:791 [6] getindex @ ~/.julia/packages/DataFrames/kcA9R/src/other/index.jl:446 [inlined] [7] groupby(df::DataFrames.DataFrame, cols::Vector{Symbol}; sort::Nothing, skipmissing::Bool) @ DataFrames ~/.julia/packages/DataFrames/kcA9R/src/groupeddataframe/groupeddataframe.jl:241 [8] groupby(df::DataFrames.DataFrame, cols::Vector{Symbol}) @ DataFrames ~/.julia/packages/DataFrames/kcA9R/src/groupeddataframe/groupeddataframe.jl:218 [9] top-level scope @ two_stage_analysis.md:146 [10] eval @ ./boot.jl:430 [inlined] [11] #60 @ ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:803 [inlined] [12] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [13] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:802 [14] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [15] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:522 [16] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger) @ Base.CoreLogging ./logging/logging.jl:632 [17] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [18] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:801

failed to run `@example` block in src/generated/tutorial/two_stage_analysis.md:168-187 ```@example two_stage_analysis # Set the size of the time bins for the topoplot series bin_size = 0.1 f_effects = Figure(size = (1200, 600)) tp_effects = plot_topoplotseries!( f_effects, aggregated_effects, bin_size, positions = pos2d, mapping = (; y = :yhat_mean, row = :continuous), visual = (; enlarge = 0.6, label_scatter = false, colorrange = (-3, 3)), ) ax = current_axis() linkaxes!(tp_effects.content[1:end-2]...) xlims!(ax, 0, 0.9) ylims!(ax, 0, 0.9) current_figure() ``` exception = UndefVarError: `aggregated_effects` not defined in `Main.__atexample__named__two_stage_analysis` Suggestion: check for spelling errors or missing imports. Stacktrace: [1] top-level scope @ two_stage_analysis.md:173 [2] eval @ ./boot.jl:430 [inlined] [3] #60 @ ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:803 [inlined] [4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:802 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [7] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:522 [8] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger) @ Base.CoreLogging ./logging/logging.jl:632 [9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:801

failed to run `@example` block in src/generated/tutorial/two_stage_analysis.md:198-221 ```@example two_stage_analysis # Extract the spline coefficients for the `continuous` predictor variable # from the Unfold models of all subjects basisname = unique(effects_all_subjects.basisname) coefs = extract_coefs(models.unfoldmodel, :continuous, basisname) # Conduct a one-sample Hotelling's T² test separately for all channels and time points # and compute a p-value. We compare the spline coefficients vector against 0. p_values = mapslices(c -> pvalue(OneSampleHotellingT2Test(c', [0, 0, 0])), coefs, dims = (3, 4)) |> x -> dropdims(x, dims = (3, 4)); times = unique(effects_all_subjects.time) channels = axes(p_values, 1) # For visualization purposes, save the p_values in a data frame together with time and channel p_values_df = DataFrame( channel = repeat(channels, outer = length(times)), time = repeat(times, inner = length(channels)), p_values = p_values[:], ); first(p_values_df, 5) ``` exception = ArgumentError: column name :basisname not found in the data frame Stacktrace: [1] lookupname @ ~/.julia/packages/DataFrames/kcA9R/src/other/index.jl:431 [inlined] [2] getindex @ ~/.julia/packages/DataFrames/kcA9R/src/other/index.jl:440 [inlined] [3] getindex(df::DataFrames.DataFrame, ::typeof(!), col_ind::Symbol) @ DataFrames ~/.julia/packages/DataFrames/kcA9R/src/dataframe/dataframe.jl:557 [4] getproperty(df::DataFrames.DataFrame, col_ind::Symbol) @ DataFrames ~/.julia/packages/DataFrames/kcA9R/src/abstractdataframe/abstractdataframe.jl:448 [5] top-level scope @ two_stage_analysis.md:201 [6] eval @ ./boot.jl:430 [inlined] [7] #60 @ ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:803 [inlined] [8] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [9] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:802 [10] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [11] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:522 [12] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger) @ Base.CoreLogging ./logging/logging.jl:632 [13] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [14] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:801

failed to run `@example` block in src/generated/tutorial/two_stage_analysis.md:225-244 ```@example two_stage_analysis bin_size = 0.1 f_pvalues = Figure(size = (1200, 200)) tp_pvalues = plot_topoplotseries!( f_pvalues, p_values_df, bin_size, positions = pos2d, mapping = (; y = :p_values), visual = (; enlarge = 0.6, label_scatter = false, colorrange = (0, 0.1)), colorbar = (; label = "p-value"), ) ax = current_axis() linkaxes!(tp_pvalues.content[1:end-2]...) xlims!(ax, 0, 0.9) ylims!(ax, 0, 0.9) current_figure() ``` exception = UndefVarError: `p_values_df` not defined in `Main.__atexample__named__two_stage_analysis` Suggestion: check for spelling errors or missing imports. Stacktrace: [1] top-level scope @ two_stage_analysis.md:229 [2] eval @ ./boot.jl:430 [inlined] [3] #60 @ ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:803 [inlined] [4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:802 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [7] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:522 [8] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger) @ Base.CoreLogging ./logging/logging.jl:632 [9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:801