Skip to content

[internals] Pimp up pohar perme #257

[internals] Pimp up pohar perme

[internals] Pimp up pohar perme #257

Triggered via pull request May 24, 2024 10:27
Status Failure
Total duration 2m 56s
Artifacts

CI.yml

on: pull_request
Matrix: test
Fit to window
Zoom out
Zoom in

Annotations

12 errors
Julia 1.9 - ubuntu-latest - x64 - pull_request
Process completed with exit code 1.
Julia 1.10 - ubuntu-latest - x64 - pull_request
Process completed with exit code 1.
Documentation: ../../../.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl#L44
failed to run `@example` block in src/benches.md:16-70 ```@example 1 using RateTables, NetSurvival, RCall, DataFrames function test_surv(r_method,::Type{E}, stratified) where E if stratified jl = @timed fit(E, @formula(Surv(time,status)~sex), colrec, slopop) @rput r_method r = @timed R""" rez = relsurv::rs.surv(survival::Surv(time, stat) ~ sex, rmap=list(age = age, sex = sex, year = diag), data = relsurv::colrec, ratetable = relsurv::slopop, method = r_method, add.times=1:8149) """ else jl = @timed fit(E, @formula(Surv(time,status)~1), colrec, slopop) @rput r_method r = @timed R""" rez = relsurv::rs.surv(survival::Surv(time, stat) ~ 1, rmap=list(age = age, sex = sex, year = diag), data = relsurv::colrec, ratetable = relsurv::slopop, method = r_method, add.times=1:8149) """ end return r.time / jl.time end function test_graffeo(stratified) if stratified jl = @timed fit(GraffeoTest, @formula(Surv(time,status)~stage+Strata(sex)), colrec, slopop) r = @timed R""" rez = relsurv::rs.diff(survival::Surv(time, stat) ~ stage + survival::strata(sex), rmap=list(age = age, sex = sex, year = diag), data = relsurv::colrec, ratetable = relsurv::slopop) """ else jl = @timed fit(GraffeoTest, @formula(Surv(time,status)~stage), colrec, slopop) r = @timed R""" rez = relsurv::rs.diff(survival::Surv(time, stat) ~ stage, rmap=list(age = age, sex = sex, year = diag), data = relsurv::colrec, ratetable = relsurv::slopop) """ end return r.time / jl.time end test_all(stratified) = [ test_surv("pohar-perme", PoharPerme, stratified), test_surv("ederer1", EdererI, stratified), test_surv("ederer2", EdererII, stratified), test_surv("hakulinen", Hakulinen, stratified), test_graffeo(stratified), ] test_all() = DataFrame( Algorithm = ["Pohar Perme", "EdererI", "EdererII", "Hakulinen", "Graffeo's LRT"], unstratified = test_all(false), stratified = test_all(true) ) rez = test_all() rez = test_all() # discard first run. # note: to obtain the pretty printing from the readme, you need to install PrettyTables.jl and do : # using PrettyTables # pretty_table(rez, backend = Val(:markdown)) rez ``` exception = UndefVarError: `age` not defined Stacktrace: [1] Λ!(::Type{NetSurvival.PoharPermeMethod}, ∂Nₑ::Vector{Float64}, Yₑ::Vector{Float64}, ∂Nₚ::Vector{Float64}, Yₚ::Vector{Float64}, ∂V::Vector{Float64}, T::Vector{Float64}, Δ::Vector{Float64}, a::Vector{Float64}, d::Vector{Float64}, rate_preds::DataFrames.DataFrame, ratetable::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}, grid::Vector{Float64}, ∂t::Vector{Float64}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/PoharPerme.jl:22 [2] Λ(::Type{NetSurvival.PoharPermeMethod}, T::Vector{Float64}, Δ::Vector{Float64}, age::Vector{Float64}, year::Vector{Float64}, rate_preds::DataFrames.DataFrame, ratetable::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}, grid::Vector{Float64}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/NPNSEstimator.jl:30 [3] PoharPerme(T::Vector{Float64}, Δ::Vector{Float64}, age::Vector{Float64}, year::Vector{Float64}, rate_preds::DataFrames.DataFrame, ratetable::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/NPNSEstimator.jl:11 [4] fit(::Type{PoharPerme}, formula::StatsModels.FormulaTerm{StatsModels.FunctionTerm{typeof(Surv), Vector{StatsModels.Term}}, StatsModels.ConstantTerm{Int64}}, df::DataFrames.DataFrame, rt::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}})
Documentation: ../../../.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl#L44
failed to run `@example` block in src/example.md:142-144 ```@example 2 pp = fit(PoharPerme, @formula(Surv(time5,status5)~1), colrec, slopop) ``` exception = UndefVarError: `age` not defined Stacktrace: [1] Λ!(::Type{NetSurvival.PoharPermeMethod}, ∂Nₑ::Vector{Float64}, Yₑ::Vector{Float64}, ∂Nₚ::Vector{Float64}, Yₚ::Vector{Float64}, ∂V::Vector{Float64}, T::Vector{Float64}, Δ::Vector{Float64}, a::Vector{Float64}, d::Vector{Float64}, rate_preds::DataFrames.DataFrame, ratetable::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}, grid::Vector{Float64}, ∂t::Vector{Float64}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/PoharPerme.jl:22 [2] Λ(::Type{NetSurvival.PoharPermeMethod}, T::Vector{Float64}, Δ::Vector{Float64}, age::Vector{Float64}, year::Vector{Float64}, rate_preds::DataFrames.DataFrame, ratetable::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}, grid::Vector{Float64}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/NPNSEstimator.jl:30 [3] PoharPerme(T::Vector{Float64}, Δ::Vector{Float64}, age::Vector{Float64}, year::Vector{Float64}, rate_preds::DataFrames.DataFrame, ratetable::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/NPNSEstimator.jl:11 [4] fit(::Type{PoharPerme}, formula::StatsModels.FormulaTerm{StatsModels.FunctionTerm{typeof(Surv), Vector{StatsModels.Term}}, StatsModels.ConstantTerm{Int64}}, df::DataFrames.DataFrame, rt::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/NPNSEstimator.jl:49 [5] top-level scope @ example.md:143 [6] eval @ ./boot.jl:385 [inlined] [7] #58 @ ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:754 [inlined] [8] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [9] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:753 [10] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [11] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [12] with_logger @ ./logging.jl:627 [inlined] [13] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [14] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752
Documentation: ../../../.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl#L44
failed to run `@example` block in src/example.md:148-151 ```@example 2 crude_pp = CrudeMortality(pp) println(crude_pp.Λₒ[1826], " , ", crude_pp.Λₑ[1826], " , ", crude_pp.Λₚ[1826]) ``` exception = UndefVarError: `pp` not defined Stacktrace: [1] top-level scope @ example.md:149 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752
Documentation: ../../../.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl#L44
failed to run `@example` block in src/example.md:157-168 ```@example 2 conf_int = confint(pp; level = 0.05) lower_bounds = [lower[1] for lower in conf_int] upper_bounds = [upper[2] for upper in conf_int] p1 = plot(pp.grid, pp.Sₑ, ribbon=(pp.Sₑ - lower_bounds, upper_bounds - pp.Sₑ), xlab = "Time (days)", ylab = "Net survival", label = false) p2 = plot(pp.grid, crude_pp.Λₑ, label = "Excess Mortality Rate") p2 = plot!(pp.grid, crude_pp.Λₚ, label = "Population Mortality Rate") plot(p1,p2) ``` exception = UndefVarError: `pp` not defined Stacktrace: [1] top-level scope @ example.md:158 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752
Documentation: ../../../.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl#L44
failed to run `@example` block in src/example.md:176-180 ```@example 2 pp_sex = fit(PoharPerme, @formula(Surv(time5,status5)~sex), colrec, slopop) pp_males = pp_sex[pp_sex.sex .== :male,:estimator][1] pp_females = pp_sex[pp_sex.sex .== :female,:estimator][1] ``` exception = UndefVarError: `age` not defined Stacktrace: [1] _combine(gd::DataFrames.GroupedDataFrame{DataFrames.DataFrame}, cs_norm::Vector{Any}, optional_transform::Vector{Bool}, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/58MUJ/src/groupeddataframe/splitapplycombine.jl:755 [2] _combine_prepare_norm(gd::DataFrames.GroupedDataFrame{DataFrames.DataFrame}, cs_vec::Vector{Any}, keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/58MUJ/src/groupeddataframe/splitapplycombine.jl:87 [3] _combine_prepare(gd::DataFrames.GroupedDataFrame{DataFrames.DataFrame}, ::Base.RefValue{Any}; keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/58MUJ/src/groupeddataframe/splitapplycombine.jl:52 [4] _combine_prepare @ ~/.julia/packages/DataFrames/58MUJ/src/groupeddataframe/splitapplycombine.jl:26 [inlined] [5] combine @ ~/.julia/packages/DataFrames/58MUJ/src/groupeddataframe/splitapplycombine.jl:857 [inlined] [6] fit(::Type{PoharPerme}, formula::StatsModels.FormulaTerm{StatsModels.FunctionTerm{typeof(Surv), Vector{StatsModels.Term}}, StatsModels.Term}, df::DataFrames.DataFrame, rt::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/NPNSEstimator.jl:54 [7] top-level scope @ example.md:177 [8] eval @ ./boot.jl:385 [inlined] [9] #58 @ ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:754 [inlined] [10] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [11] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:753 [12] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [13] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [14] with_logger @ ./logging.jl:627 [inlined] [15] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [16] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752
Documentation: ../../../.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl#L44
failed to run `@example` block in src/example.md:184-186 ```@example 2 test_sex = fit(GraffeoTest, @formula(Surv(time5,status5)~sex), colrec, slopop) ``` exception = UndefVarError: `age` not defined Stacktrace: [1] Λ!(::Type{NetSurvival.PoharPermeMethod}, ∂Nₑ::Vector{Float64}, Yₑ::Vector{Float64}, ∂Nₚ::Vector{Float64}, Yₚ::Vector{Float64}, ∂V::Vector{Float64}, T::Vector{Float64}, Δ::Vector{Float64}, a::Vector{Float64}, d::Vector{Float64}, rate_preds::DataFrames.DataFrame, ratetable::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}, grid::Vector{Float64}, ∂t::Vector{Float64}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/PoharPerme.jl:22 [2] GraffeoTest(T::Vector{Float64}, Δ::Vector{Float64}, age::Vector{Float64}, year::Vector{Float64}, rate_preds::DataFrames.DataFrame, strata::Vector{Union{Missing, Int64}}, group::Vector{Union{Missing, Int64}}, ratetable::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/GraffeoTest.jl:101 [3] fit(::Type{GraffeoTest}, formula::StatsModels.FormulaTerm{StatsModels.FunctionTerm{typeof(Surv), Vector{StatsModels.Term}}, StatsModels.Term}, df::DataFrames.DataFrame, rt::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/GraffeoTest.jl:158 [4] top-level scope @ example.md:185 [5] eval @ ./boot.jl:385 [inlined] [6] #58 @ ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:754 [inlined] [7] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [8] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:753 [9] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [10] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [11] with_logger @ ./logging.jl:627 [inlined] [12] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [13] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752
Documentation: ../../../.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl#L44
failed to run `@example` block in src/example.md:192-197 ```@example 2 colrec.age65 .= ifelse.(colrec.age .>= 65*365.241, :old, :young) pp_age65 = fit(PoharPerme, @formula(Surv(time5,status5)~age65), colrec, slopop) pp_young = pp_age65[pp_age65.age65 .== :young, :estimator][1] pp_old = pp_age65[pp_age65.age65 .== :old, :estimator][1] ``` exception = UndefVarError: `age` not defined Stacktrace: [1] _combine(gd::DataFrames.GroupedDataFrame{DataFrames.DataFrame}, cs_norm::Vector{Any}, optional_transform::Vector{Bool}, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/58MUJ/src/groupeddataframe/splitapplycombine.jl:755 [2] _combine_prepare_norm(gd::DataFrames.GroupedDataFrame{DataFrames.DataFrame}, cs_vec::Vector{Any}, keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/58MUJ/src/groupeddataframe/splitapplycombine.jl:87 [3] _combine_prepare(gd::DataFrames.GroupedDataFrame{DataFrames.DataFrame}, ::Base.RefValue{Any}; keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/58MUJ/src/groupeddataframe/splitapplycombine.jl:52 [4] _combine_prepare @ ~/.julia/packages/DataFrames/58MUJ/src/groupeddataframe/splitapplycombine.jl:26 [inlined] [5] combine @ ~/.julia/packages/DataFrames/58MUJ/src/groupeddataframe/splitapplycombine.jl:857 [inlined] [6] fit(::Type{PoharPerme}, formula::StatsModels.FormulaTerm{StatsModels.FunctionTerm{typeof(Surv), Vector{StatsModels.Term}}, StatsModels.Term}, df::DataFrames.DataFrame, rt::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/NPNSEstimator.jl:54 [7] top-level scope @ example.md:194 [8] eval @ ./boot.jl:385 [inlined] [9] #58 @ ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:754 [inlined] [10] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [11] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:753 [12] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [13] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [14] with_logger @ ./logging.jl:627 [inlined] [15] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [16] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752
Documentation: ../../../.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl#L44
failed to run `@example` block in src/example.md:205-207 ```@example 2 test_age65 = fit(GraffeoTest, @formula(Surv(time5,status5)~age65), colrec, slopop) ``` exception = UndefVarError: `age` not defined Stacktrace: [1] Λ!(::Type{NetSurvival.PoharPermeMethod}, ∂Nₑ::Vector{Float64}, Yₑ::Vector{Float64}, ∂Nₚ::Vector{Float64}, Yₚ::Vector{Float64}, ∂V::Vector{Float64}, T::Vector{Float64}, Δ::Vector{Float64}, a::Vector{Float64}, d::Vector{Float64}, rate_preds::DataFrames.DataFrame, ratetable::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}, grid::Vector{Float64}, ∂t::Vector{Float64}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/PoharPerme.jl:22 [2] GraffeoTest(T::Vector{Float64}, Δ::Vector{Float64}, age::Vector{Float64}, year::Vector{Float64}, rate_preds::DataFrames.DataFrame, strata::Vector{Union{Missing, Int64}}, group::Vector{Union{Missing, Int64}}, ratetable::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/GraffeoTest.jl:101 [3] fit(::Type{GraffeoTest}, formula::StatsModels.FormulaTerm{StatsModels.FunctionTerm{typeof(Surv), Vector{StatsModels.Term}}, StatsModels.Term}, df::DataFrames.DataFrame, rt::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/GraffeoTest.jl:158 [4] top-level scope @ example.md:206 [5] eval @ ./boot.jl:385 [inlined] [6] #58 @ ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:754 [inlined] [7] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [8] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:753 [9] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [10] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [11] with_logger @ ./logging.jl:627 [inlined] [12] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [13] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752
Documentation: ../../../.julia/packages/Documenter/CJeWX/src/utilities/utilities.jl#L44
failed to run `@example` block in src/example.md:214-238 ```@example 2 conf_int_men = confint(pp_males; level = 0.05) lower_bounds_men = [lower[1] for lower in conf_int_men] upper_bounds_men = [upper[2] for upper in conf_int_men] conf_int_women = confint(pp_females; level = 0.05) lower_bounds_women = [lower[1] for lower in conf_int_women] upper_bounds_women = [upper[2] for upper in conf_int_women] conf_int_under65 = confint(pp_young; level = 0.05) lower_bounds_under65 = [lower[1] for lower in conf_int_under65] upper_bounds_under65 = [upper[2] for upper in conf_int_under65] conf_int_65 = confint(pp_old; level = 0.05) lower_bounds_65 = [lower[1] for lower in conf_int_65] upper_bounds_65 = [upper[2] for upper in conf_int_65] plot1 = plot(pp_males.grid, pp_males.Sₑ, ribbon=(pp_males.Sₑ - lower_bounds_men, upper_bounds_men - pp_males.Sₑ), xlab = "Time (days)", ylab = "Net survival", label = "men") plot1 = plot!(pp_females.grid, pp_females.Sₑ, ribbon=(pp_females.Sₑ - lower_bounds_women, upper_bounds_women - pp_females.Sₑ), xlab = "Time (days)", ylab = "Net survival", label = "women") plot2 = plot(pp_young.grid, pp_young.Sₑ, ribbon=(pp_young.Sₑ - lower_bounds_under65, upper_bounds_under65 - pp_young.Sₑ), xlab = "Time (days)", ylab = "Net survival", label = "Under 65") plot2 = plot!(pp_old.grid, pp_old.Sₑ, ribbon=(pp_old.Sₑ - lower_bounds_65, upper_bounds_65 - pp_old.Sₑ), xlab = "Time (days)", ylab = "Net survival", label = "65 and up") plot(plot1, plot2, layout = (1, 2)) ``` exception = UndefVarError: `pp_males` not defined Stacktrace: [1] top-level scope @ example.md:215 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752
Documentation
Process completed with exit code 1.