[internals] Pimp up pohar perme #257
Annotations
10 errors
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Run julia-actions/julia-docdeploy@v1:
../../../.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}})
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Run julia-actions/julia-docdeploy@v1:
../../../.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
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|
Run julia-actions/julia-docdeploy@v1:
../../../.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
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|
Run julia-actions/julia-docdeploy@v1:
../../../.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
|
|
Run julia-actions/julia-docdeploy@v1:
../../../.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
|
|
Run julia-actions/julia-docdeploy@v1:
../../../.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
|
|
Run julia-actions/julia-docdeploy@v1:
../../../.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
|
|
Run julia-actions/julia-docdeploy@v1:
../../../.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
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Run julia-actions/julia-docdeploy@v1:
../../../.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
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Run julia-actions/julia-docdeploy@v1
Process completed with exit code 1.
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The logs for this run have expired and are no longer available.
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